Figure 2

Patchwork performance on in silico dilutions of cancer and matched normal cell lines. TAPS (Tumor Aberration Prediction Suite) analysis of the breast-cancer cell line HCC1954 (nearly tetraploid) was used as a gold standard for the evaluation of Patchwork performance on a slightly different culture from the same cell line. Reads from the patient-matched blood cell line HCC1954BL were added to the data to estimate the effect of a reduced proportion of tumor cells. Data from the pure cancer cell line and mixtures corresponding to 70%, 50%, and 30% tumor cells were analyzed. (A) Sensitivity and (B) specificity for allele-specific copy number calls.